José N. Onuchic

发表

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Ryan L. Hayes, Jeffrey K. Noel, Mariana Levi, 2016, PLoS Comput. Biol..

Special issue on protein folding: experimental and theoretical approaches

José N. Onuchic, 2008 .

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

Bin Chen, Ryan L. Hayes, Heiko Lammert, 2017, PLoS Comput. Biol..

Molecular Electronic Shift Registers

José N. Onuchic, David N. Beratan, 1990 .

RACIPE: a computational tool for modeling gene regulatory circuits using randomization

Bin Huang, Dongya Jia, José N. Onuchic, 2017, bioRxiv.

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

Jeffrey K. Noel, José N. Onuchic, Paul C. Whitford, 2010, Nucleic Acids Res..

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function

José N. Onuchic, Paul C. Whitford, Michael A. Jamros, 2012, PLoS Comput. Biol..

Energy Landscapes of Protein Self-Assembly: Lessons from Native Topology-Based Models

José N. Onuchic, Yaakov Levy, 2007 .

Faculty Opinions recommendation of Breaking symmetry in protein dimers: designs and functions.

José N. Onuchic, 2016 .

Information storage at the molecular level - The design of a molecular shift register memory

John J. Hopfield, José N. Onuchic, David N. Beratan, 1989 .

The Dominant Folding Route Minimizes Backbone Distortion in SH3

Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, 2012, PLoS Comput. Biol..

Mechanisms of Protein Assembly and Folding: Lessons from Minimalist Models

José N. Onuchic, 2007 .

Education at the Interface -- Experiences and Perspectives

José N. Onuchic, 2010 .

The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors

Changbong Hyeon, José N. Onuchic, Biman Jana, 2012, PLoS Comput. Biol..

Pierced Lasso Bundles Are a New Class of Knot-like Motifs

Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, 2014, PLoS Comput. Biol..

Interrogating the topological robustness of gene regulatory circuits by randomization

Bin Huang, Dongya Jia, Eshel Ben-Jacob, 2016, bioRxiv.

Towards rationally redesigning bacterial signaling systems using information encoded in abundant sequence data

José N. Onuchic, Herbert Levine, Faruck Morcos, 2014 .

Faculty Opinions recommendation of Sequence co-evolution gives 3D contacts and structures of protein complexes.

José N. Onuchic, 2016 .

Deciding fate in adverse times: Sporulation and competence in Bacillus subtilis

Peter G. Wolynes, José N. Onuchic, Daniel Schultz, 2009, Proceedings of the National Academy of Sciences.

Faculty Opinions recommendation of A many-body term improves the accuracy of effective potentials based on protein coevolutionary data.

José N. Onuchic, 2016 .

Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity

José N. Onuchic, Biman Jana, J. Onuchic, 2016, PLoS Comput. Biol..

A Stevedore's Protein Knot

Joanna I. Sulkowska, Hsiao-Ping Hsu, José N. Onuchic, 2010, PLoS Comput. Biol..

Rapid assessment of T-cell receptor specificity of the immune repertoire

Cecilia Clementi, José N. Onuchic, Xingcheng Lin, 2021 .

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Peter G. Wolynes, José N. Onuchic, Vinícius G. Contessoto, 2019, bioRxiv.

Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill

Jianpeng Ma, Jeffrey K. Noel, José N. Onuchic, 2018, Proceedings of the National Academy of Sciences.

Allostery in the ferredoxin protein motif does not involve a conformational switch

Heiko Lammert, José N. Onuchic, Paul C. Whitford, 2011, Proceedings of the National Academy of Sciences.

Structural and energetic heterogeneity in protein folding. I. Theory

José N. Onuchic, Steven S. Plotkin, J. Onuchic, 2002 .

SCIENCE EDUCATION: Enhanced: Educating Future Scientists

José N. Onuchic, Elizabeth D. Getzoff, Nancy J. Kopell, 2003 .

Mapping electron tunneling pathways: an algorithm that finds the "minimum length"/maximum coupling pathway between electron donors and acceptors in proteins

José N. Onuchic, David N. Beratan, Jonathan N. Betts, 1992 .

Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem

Margaret S. Cheung, José N. Onuchic, J. Onuchic, 2003 .

Folding Circular Permutants of IL-1β: Route Selection Driven by Functional Frustration

José N. Onuchic, Patricia A. Jennings, Shachi Gosavi, 2012, PloS one.

Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins

Margaret S. Cheung, Anatoly B. Kolomeisky, Michael R. Diehl, 2017, Proceedings of the National Academy of Sciences.

Protein electron transport: single versus multiple pathways

José N. Onuchic, David N. Beratan, J. Onuchic, 1993 .

Operating principles of Notch–Delta–Jagged module of cell–cell communication

Cecilia Clementi, Eshel Ben-Jacob, José N. Onuchic, 2015 .

Proteins at Work

José N. Onuchic, Paul C. Whitford, Michael A. Jamros, 2010, The Journal of Biological Chemistry.

Knotting a Protein in Explicit Solvent

Joanna I. Sulkowska, Jeffrey K. Noel, José N. Onuchic, 2014 .

Connection between Simple Models and Quantum Chemical Models for Electron-Transfer Tunneling Matrix Element Calculations: A Dyson's Equations-Based Approach

José N. Onuchic, Ilya A. Balabin, 1996 .

MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination

Eshel Ben-Jacob, José N. Onuchic, Mingyang Lu, 2013, Proceedings of the National Academy of Sciences.

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

Eshel Ben-Jacob, José N. Onuchic, Mingyang Lu, 2015, Front. Oncol..

Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions

Peter G. Wolynes, José N. Onuchic, J. Onuchic, 1999 .

Electron tunneling pathways in ruthenated proteins

José N. Onuchic, David N. Beratan, Harry B. Gray, 1990 .

Coevolutionary signals across protein lineages help capture multiple protein conformations

Terence Hwa, José N. Onuchic, Faruck Morcos, 2013, Proceedings of the National Academy of Sciences.

Braiding topology and the energy landscape of chromosome organization proteins

Peter G. Wolynes, José N. Onuchic, Aram Davtyan, 2019, Proceedings of the National Academy of Sciences.

Excited states of ribosome translocation revealed through integrative molecular modeling

Florence Tama, José N. Onuchic, Paul C. Whitford, 2011, Proceedings of the National Academy of Sciences.

Energy Landscape Analysis of Protein Dimers

Peter G. Wolynes, José N. Onuchic, Yaakov Levy, 2004 .

Jamming Proteins with Slipknots and Their Free Energy Landscape

Joanna I. Sulkowska, José N. Onuchic, Piotr Sułkowski, 2010 .

Nonlinear susceptibilities of finite conjugated organic polymers

José N. Onuchic, Joseph W. Perry, David N. Beratan, 1987 .

Design of a True Molecular Electronic Device: The Electron Transfer Shift Register Memory

John J. Hopfield, José N. Onuchic, David N. Beratan, 1989 .

Knotting a Protein in Explicit Solvent

Joanna I. Sulkowska, Jeffrey K. Noel, José N. Onuchic, 2013 .

A predictive theoretical model for electron tunneling pathways in proteins

José N. Onuchic, David N. Beratan, J. Onuchic, 1990 .

Electron tunneling through covalent and noncovalent pathways in proteins

John J. Hopfield, José N. Onuchic, David N. Beratan, 1987 .

The energy landscape for protein folding and possible connections to function

Margaret S. Cheung, José N. Onuchic, Leslie L. Chavez, 2004 .

Educating future scientists

José N. Onuchic, Elizabeth D. Getzoff, Nancy J. Kopell, 2001, Nature.

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

José N. Onuchic, Herbert Levine, Faruck Morcos, 2014, Proceedings of the National Academy of Sciences.

Electron tunneling pathways in proteins : a method to compute tunneling matrix elements in very large systems

José N. Onuchic, David N. Beratan, J. Onuchic, 1991 .

Estimation of Residue-Residue Coevolution using Direct Coupling Analysis Identifies Many Native Contacts Across a Large Number of Domain Families

Debora S. Marks, Chris Sander, Terence Hwa, 2012 .

The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin

José N. Onuchic, Patricia A. Jennings, Ellinor Haglund, 2012, PloS one.

Effect of gatekeepers on the early folding kinetics of a model β-barrel protein

Charles L. Brooks, José N. Onuchic, J. Onuchic, 2003 .

Forging tools for refining predicted protein structures

Wei Lu, Xun Chen, Mingchen Chen, 2019, Proceedings of the National Academy of Sciences.